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- PDB-8jct: Crystal structure of fungal cutinase from Aspergillus fumigatiaffinis -

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Basic information

Entry
Database: PDB / ID: 8jct
TitleCrystal structure of fungal cutinase from Aspergillus fumigatiaffinis
ComponentsCutinase
KeywordsHYDROLASE / PET hydrolase / Aspergillus fumigatiaffinis / Fungal cutinase
Function / homology
Function and homology information


cutinase / cutinase activity / extracellular region
Similarity search - Function
Cutinase, monofunctional / Cutinase, aspartate and histidine active sites / Cutinase, serine active site / Cutinase, serine active site. / Cutinase, aspartate and histidine active sites. / Cutinase / Cutinase/acetylxylan esterase / Cutinase / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Biological speciesAspergillus fumigatiaffinis (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKim, M. / Lee, S.H. / Kim, K.-J.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Characterization and engineering of novel fungal PET degrading enzyme from Aspergillus fumigatiaffinis
Authors: Lee, S.H. / Kim, M. / Kim, K.J.
History
DepositionMay 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cutinase


Theoretical massNumber of molelcules
Total (without water)20,9791
Polymers20,9791
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.053, 63.053, 215.316
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-217-

HOH

21A-219-

HOH

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Components

#1: Protein Cutinase


Mass: 20978.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatiaffinis (mold) / Gene: CNMCM6457_007885, CNMCM6805_005550 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8H4MGN0, cutinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 25% PEG3350, 0.1 M HEPES pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 4184 / % possible obs: 96.4 % / Redundancy: 4.5 % / CC1/2: 0.984 / CC star: 0.996 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.051 / Rrim(I) all: 0.119 / Χ2: 1.968 / Net I/σ(I): 8.9 / Num. measured all: 18705
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.8-2.852.70.3072050.7030.9080.20.3691.0395.8
2.85-2.92.90.3221970.5520.8440.1950.381.21490.8
2.9-2.963.20.2961940.6680.8950.1750.3461.21294.6
2.96-3.023.60.2652040.7380.9220.1480.3061.05195.3
3.02-3.083.10.2921970.6380.8830.1850.3481.293.4
3.08-3.153.80.2292030.8420.9560.1220.2611.68995.8
3.15-3.233.90.2221930.8430.9560.1180.2531.53993.7
3.23-3.323.90.2032190.9110.9770.1060.231.42997.8
3.32-3.423.90.1771930.9660.9910.0930.21.47795.1
3.42-3.534.50.1562120.9630.9910.0780.1751.6696.8
3.53-3.654.70.1482110.9810.9950.0690.1641.75398.1
3.65-3.85.50.1292010.9810.9950.0580.1411.93999
3.8-3.9750.1142070.9890.9970.0530.1262.00596.3
3.97-4.184.90.1122150.9880.9970.050.1232.27397.3
4.18-4.445.70.1012180.9910.9980.0430.112.62998.6
4.44-4.795.40.0982100.9940.9990.0420.1072.52397.7
4.79-5.275.70.0922140.9930.9980.040.1012.18597.3
5.27-6.035.40.0912190.9930.9980.040.12.14498.2
6.03-7.595.70.0822250.9930.9980.0360.092.28299.6
7.59-505.30.062470.9950.9990.0280.0672.8896.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OHY

4ohy


Resolution: 2.8→33.84 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.898 / SU B: 21.51 / SU ML: 0.384 / Cross valid method: THROUGHOUT / ESU R Free: 0.469 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27537 199 4.8 %RANDOM
Rwork0.1723 ---
obs0.17735 3985 96.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.066 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å2-0.31 Å20 Å2
2---0.62 Å2-0 Å2
3---2.03 Å2
Refinement stepCycle: 1 / Resolution: 2.8→33.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1375 0 0 19 1394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121403
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161345
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.6431909
X-RAY DIFFRACTIONr_angle_other_deg0.3731.5633102
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7325188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.80857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.03410218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0480.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021659
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02301
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0944.751755
X-RAY DIFFRACTIONr_mcbond_other3.0924.752755
X-RAY DIFFRACTIONr_mcangle_it4.9118.53942
X-RAY DIFFRACTIONr_mcangle_other4.9118.532943
X-RAY DIFFRACTIONr_scbond_it3.595.25648
X-RAY DIFFRACTIONr_scbond_other3.5865.245647
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0789.514968
X-RAY DIFFRACTIONr_long_range_B_refined8.42844.61570
X-RAY DIFFRACTIONr_long_range_B_other8.42644.541569
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.801→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 13 -
Rwork0.294 294 -
obs--93.31 %

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